[gmx-users] Re: Free energy calculation question

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 31 20:18:10 CEST 2011

Fabian Casteblanco wrote:
> Hello Justin,
> I'm looking at the dG vs Lambda plot that is an output from G_bar but
> on the Shirts et al paper that you included, the part where it talks
> about linearity, it is referring to dH/dLambda for electrostatic
> decoupling.  So if I take the line formed by dGtotal vs Lambda from
> g_bar output and take the derivative excluding the beginning and end
> parts (lambda approaches 0 and 1) then it does seem to take more of a
> somewhat linear shape.  If you can see attached, I think perhaps thats

You haven't attached anything.

> how I was misreading it?  I hope that can be the reason, since I've
> done it with 4 different cases (2 different amount of solvent
> molecules and using MD and SD integrator) and they all seem to be
> giving similar results.

That could be it.  The BAR output and the plots from TI are different.  Also be 
sure that you're not using soft-core for the Coulombic (de)coupling, as was 
suggested previously.


> Thanks for your help.
> -Fabian
> On Wed, Aug 31, 2011 at 11:24 AM, Fabian Casteblanco
> <fabian.casteblanco at gmail.com> wrote:
>> Hello Justin,
>> I'm calculating the free energy of a drug in an alcohol solvent.  I
>> have a question referring to your free energy tutorial.  You mentioned
>> that decoupling of electrostatic interactions is linear and decoupling
>> of vdW can vary.  Is this true for your case of methanol in water or
>> for all cases?  When I ran my system of drug in ethanol solvent, I got
>> a non linear dG for both electrostatic and vdW.  Also, is there no
>> need to find dG of cav ( the free energy required to form the solute
>> cavity within the solvent) ?  I have attached some graphs.
>> Thanks for your help.  Your tutorial was extremely useful.
>> --
>> Best regards,
>> Fabian F. Casteblanco
>> Rutgers University --
>> Chemical Engineering PhD Student
>> C: +908 917 0723
>> E:  fabian.casteblanco at gmail.com


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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